More about the differences between Hadoop and HBase - I think that having Hadoop will be enough for this exercise: if I understand correctly, skale (as well as Shark) evaluate the plain data stored in Hadoop in-memory instead of files, but I am not sure:

Now, the data will be stored as files (very much like a simple mongoDB format with no schema at all). HBase is one of the many ways to give a schema or ordering to the no-structured data. All the existing options that run on top of HDFS (Cassandra, for example) seems to provide different advantages and disadvantages.